LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further informatio...e J#. Chromosome-scale scaffolding of de novo genome a...2246 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...ontains thousands of sparsely sequenced long fragments ranging fro...ation for scaffolding de novo genome assemblies. FragScaff is comp...rate chromosome-scale de novo genome assemblies without the need f...J#. In vitro, long-range sequence information for de novo genome assembly via transposase contig...2246 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
...ation, please cite the following reference:Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 12553...2246 days ago
2246 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just wo...t and accurate haplotype assembly for diverse sequencing technologies. Genome Res. gr.213462.116 (2016). doi:...2245 days ago
Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome a...2245 days ago
2245 days ago
Hapsembler: An Assembler for Highly Polymorphic Genomes
Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. http://compbio.cs.toronto.edu/hapsembler/2238 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex p...le description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of e...2238 days ago
2237 days ago